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A systematic evaluation of the data processing methods is crucial to identify adequate processing procedures for a given experimental setup. Current comparative studies are mostly focused on peak area data but not on absolute concentrations. In this study, we evaluated data processing methods to produce outputs that were most similar to the corresponding absolute quantified data. We examined the data distribution characteristics, fold difference patterns between 2 metabolites, and sample variance. We used 2 metabolomic datasets from a retail milk study and a lupus nephritis cohort as test cases. When studying the impact of data normalization, transformation, scaling, and combinations of these methods, we found that the cross-contribution compensating multiple standard normalization (ccmn) method, followed by square root data transformation, was most appropriate for a well-controlled study such as the milk study dataset. Regarding the lupus nephritis cohort study, only ccmn normalization could slightly improve the data quality of the noisy cohort. Since the assessment accounted for the resemblance between processed data and the corresponding absolute quantified data, our results denote a helpful guideline for processing metabolomic datasets within a similar context (food and clinical metabolomics). Finally, we introduce Metabox 2.0, which enables thorough analysis of metabolomic data, including data processing, biomarker analysis, integrative analysis, and data interpretation. It was successfully used to process and analyze the data in this study. An online web version is available at http:\/\/metsysbio.com\/metabox.<\/jats:p>","DOI":"10.1093\/gigascience\/giae005","type":"journal-article","created":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T12:39:10Z","timestamp":1710506350000},"source":"Crossref","is-referenced-by-count":17,"title":["Data processing solutions to render metabolomics more quantitative: case studies in food and clinical metabolomics using Metabox 2.0"],"prefix":"10.1093","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0245-0833","authenticated-orcid":false,"given":"Kwanjeera","family":"Wanichthanarak","sequence":"first","affiliation":[{"name":"Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]},{"name":"Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9618-6473","authenticated-orcid":false,"given":"Ammarin","family":"In-on","sequence":"additional","affiliation":[{"name":"Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]},{"name":"Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sili","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of California Davis , Davis, CA 95616 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6261-8928","authenticated-orcid":false,"given":"Oliver","family":"Fiehn","sequence":"additional","affiliation":[{"name":"West Coast Metabolomics Center, University of California Davis Genome Center , Davis, CA 95616 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4536-4492","authenticated-orcid":false,"given":"Arporn","family":"Wangwiwatsin","sequence":"additional","affiliation":[{"name":"Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University , Khon Kaen 40002 ,","place":["Thailand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9461-8597","authenticated-orcid":false,"given":"Sakda","family":"Khoomrung","sequence":"additional","affiliation":[{"name":"Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]},{"name":"Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]},{"name":"Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok 10700 ,","place":["Thailand"]},{"name":"Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University , Bangkok 10700 ,","place":["Thailand"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,3,15]]},"reference":[{"key":"2024111706301299100_bib1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.copbio.2015.09.004","article-title":"Food metabolomics: from farm to human","volume":"37","author":"Kim","year":"2016","journal-title":"Curr Opin Biotechnol"},{"key":"2024111706301299100_bib2","doi-asserted-by":"crossref","first-page":"474","DOI":"10.3389\/fphar.2017.00474","article-title":"Metabolomics and integrative omics for the development of Thai traditional medicine","volume":"8","author":"Khoomrung","year":"2017","journal-title":"Front Pharmacol"},{"issue":"4","key":"2024111706301299100_bib3","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1152\/physrev.00035.2018","article-title":"Metabolomics for investigating physiological and pathophysiological processes","volume":"99","author":"Wishart","year":"2019","journal-title":"Physiol Rev"},{"issue":"3","key":"2024111706301299100_bib4","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s10545-017-0074-y","article-title":"Advances in metabolome information retrieval: turning chemistry into biology. 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